Workflow

This workflow is for generating the baseline nanopore variant calls for the project. The main result is the concordance plots that will compare the SNP calls obtained from bcftools on Nanopore data and those from the COMPASS pipeline for Illumina.

Click the nodes to obtain details about each step.

Distance

Data

Plot

Mixed Tech

Dotplot

Self

Truth Evaluation

Other

Raw data

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

Configuration files
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samplesheet:     "../../docs/samplesheet.csv"
compass_vcf_dir: "illumina/gvcfs"
asm_dir:         "../assembly/results"
data_dir:        "../../data/QC/subsampled"
genome_size:     4411532
h37rv:
  genome: "resources/h37rv.fa"
  mask:   "resources/compass-mask.bed"
containers:
  conda:     "docker://continuumio/miniconda3:4.7.12"
  bcftools:  "docker://quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
  varifier:  "docker://quay.io/iqballab/varifier:3c8152a"
  snp-dists: "docker://quay.io/biocontainers/snp-dists:0.7.0--hed695b0_0"
  psdm:      "docker://quay.io/mbhall88/psdm:0.1.0"
  samtools:  "docker://quay.io/biocontainers/samtools:1.13--h8c37831_0"
  happy:     "docker://quay.io/biocontainers/hap.py:0.3.14--py27h5c5a3ab_0"
envs:
  aln_tools:            "envs/aln_tools.yaml"
  filter:               "envs/filter.yaml"
  varifier:             "envs/varifier.yaml"
  concordance:          "envs/concordance.yaml"
  consensus:            "envs/consensus.yaml"
  dotplot:              "envs/dotplot.yaml"
  plot_concordance:     "envs/plot_concordance.yaml"
  plot_truth_eval:      "envs/plot_truth_eval.yaml"
  distance:             "envs/distance.yaml"
  plot_distance_matrix: "envs/plot_distance_matrix.yaml"
  mixed_self_distance:  "envs/mixed_self_distance.yaml"
  bcftools_dotplot:     "envs/dotplot.yaml"
  happy:                "envs/happy.yaml"
scripts:
  filter:               "scripts/apply_filters.py"
  concordance:          "scripts/concordance.py"
  consensus:            "scripts/consensus.py"
  distance:             "scripts/distance.py"
  dotplot:              "scripts/distance_dot_plot.py"
  plot_concordance:     "scripts/plot_concordance.py"
  plot_truth_eval:      "scripts/plot_truth_eval.py"
  plot_distance_matrix: "scripts/plot_distance_matrix.py"
  mixed_self_distance:  "scripts/mixed_self_distance.py"
  bcftools_dotplot:     "scripts/bcftools_dotplot.py"

# filters for nanopore bcftools calls
filters:
  min_depth:       0
  min_fed:         0
  max_depth:       0
  min_qual:        85
  min_strand_bias: 0
  min_bqb:         0
  min_mqb:         0
  min_rpb:         0
  max_sgb:         0
  min_vdb:         0
  min_mq:          0
  min_frs:         0.90
  # min_rqbz:        -2.6
  # max_rqbz:        3.0
  # max_scbz:        2.2


assemblies:
  mada_101:  "flye"
  mada_102:  "flye"
  mada_104:  "flye"
  mada_130:  "flye"
  mada_116:  "flye"
  mada_1-44: "flye"
  mada_132:  "flye"
  mada_125:  "flye"

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